Reproductive health education (RHE) programmes in schools are a well-recognised means of helping young people make informed decisions relating to their sexual health and well-being. Very little research however has investigated attitudes towards such programmes among students in the Arab world. A national HIV education curriculum was developed in Lebanon in 2005. However, in the context of competing priorities and mixed levels of social resistance, curriculum implementation to date is far from universal. This study aimed to determine the prevalence of support for school-based RHE and the main factors associated with such support among young people aged 11-16 years in Lebanon. A secondary analysis of data from the 2011 Global school-based Student Health Survey (GSHS) was conducted. Students who supported RHE (58.1%) were more likely to be of higher grade level (adjusted OR [Odds Ratio] = 1.78, p-value = 0.005), to have ever drunk alcohol (adjusted OR = 1.52, p-value = 0.012), to prefer mixed classes for RHE (adjusted OR = 3.19, p-value < 0.0001), to say RHE should start before or at puberty (adjusted OR = 3.57, p-value < 0.0001), and to be exposed to more health education topics in school (adjusted OR = 1.2, p-value < 0.0001). Identifying such sub-groups in the student body should inform the equitable implementation of RHE in culturally diverse settings like Lebanon.